+ configurable controls (SPACE, ALT, ENTER, ESCAPE as gamepad-button, jump with gamepad-button instead of holding up on the dpad/stick)
+ hq2x - scaler
+ load times / savestates for immediate loading of the start of a game
+ ultra smooth scrolling when display set to 50Hz or 100Hz

Real Amiga:

+ design and feeling
+ noise of the disk drive (still better than the feature in WinUAE)
+ ultrasmooth scrolling